Tilia is a typical northern hemisphere temperate genus consisting of 25 species that are distinct in their foliaceous bracts subtending the cymose inflorescence. Chloroplast DNA sequence data suggest that Tilia is an isolated lineage from other tiliaceous genera of the Malvales. Infrageneric taxonomy of Tilia , however, has been difficult and controversial because of the lack of reliable morphological characters to differentiate species as a result of possible polyploid origin (x=41), ancient lineage history, and ease of hybridization among species. In this study sequences of low copy nuclear NIA gene introns were used to elucidate phylogenetic relationships of diploid species of Tilia . Up to 10 clones of PCR products of the NIA intron 3 were sequenced for each diploid species. Four loci were found, and sequence divergence among these loci ranged from 11.5-24.1%. Within each locus, there was one to three alleles characterized by long indels, and their averaged sequence divergences were from 2.4-4.2%. Allelic polymorphisms were observed in two loci in T. oliveri , T. americana , T. caroliniana , and T. mexicana . Phylogenetic analyses based on exon sequences of a limited length support the division of Tilia into two sections, i.e., sections Endochrysea and Tilia . However, further division of section Tilia based on fruit characters was not supported. Thin-shelled fruits appear to have evolved more than once form the ancestral state of the thick-shelled. Tilia platyphyllos is phylogenetically distant from T. cordata , though they hybridize naturally producing fertile hybrids. T. oliveri is perhaps the earliest lineage in section Tilia . North American species are closely related to T. kiusiana and European species. Phylogenetic trees based on sequences of NIA introns agree with fossil record both in space and in time, supporting the origin of Tilia from western North America, and the recent origin of North American and European species from eastern Asian lineages.

Key words: Biogeography, diploid, Nitrate reductase, Phylogeny, Tilia